test: cover file grouping for both modes plus TSV header

Author: vtorlima

package/tests/test_file_grouping.py

@@ -1,11 +1,154 @@
 """Tests for _group_files and FileReader behavior."""
 
+import json
+from pathlib import Path
 from typing import Callable
 
-from pyaslreport.modalities.asl.processor import ASLProcessor
+import pytest
 
+from pyaslreport.modalities.asl.processor import ASLProcessor, ProcessingContext
 
-def test_make_processor_factory(make_processor: Callable[..., ASLProcessor]) -> None:
-    """The make_processor fixture produces an ASLProcessor with the given files."""
-    proc = make_processor(files=[])
-    assert proc.data["files"] == []
+# ---------- _group_files: NIfTI mode (exact suffix matching) ----------
+
+
+class TestGroupFilesNiftiMode:
+    def test_groups_asl_with_tsv_and_m0(
+        self, make_processor: Callable[..., ASLProcessor], tmp_path: Path
+    ) -> None:
+        """A canonical BIDS triple groups together correctly."""
+        asl_json = tmp_path / "sub-01_asl.json"
+        asl_json.write_text(json.dumps({"M0Type": "Separate"}))
+        tsv = tmp_path / "sub-01_aslcontext.tsv"
+        tsv.write_text("volume_type\ncontrol\nlabel\n")
+        m0_json = tmp_path / "sub-01_m0scan.json"
+        m0_json.write_text(json.dumps({"EchoTime": 0.012}))
+
+        proc = make_processor(files=[str(asl_json), str(tsv), str(m0_json)])
+        groups = proc._group_files("nifti")
+
+        assert len(groups) == 1
+        g = groups[0]
+        assert g["asl_json"][0] == "sub-01_asl.json"
+        assert g["tsv"][0] == "sub-01_aslcontext.tsv"
+        assert g["m0_json"][0] == "sub-01_m0scan.json"
+
+    def test_two_sessions_produce_two_groups(
+        self, make_processor: Callable[..., ASLProcessor], tmp_path: Path
+    ) -> None:
+        """Two BIDS sessions in the same directory produce two groups."""
+        # Build the list explicitly. Do NOT scan tmp_path with iterdir(): the
+        # make_processor -> minimal_nifti_path fixture also writes asl.nii.gz
+        # into tmp_path, and _group_files rejects unknown extensions.
+        files: list[str] = []
+        for i in [1, 2]:
+            asl_json = tmp_path / f"sub-0{i}_asl.json"
+            asl_json.write_text(json.dumps({"M0Type": "Separate"}))
+            tsv = tmp_path / f"sub-0{i}_aslcontext.tsv"
+            tsv.write_text("volume_type\ncontrol\nlabel\n")
+            files.extend([str(asl_json), str(tsv)])
+        proc = make_processor(files=files)
+        groups = proc._group_files("nifti")
+        assert len(groups) == 2
+
+    def test_unsupported_extension_raises(
+        self, make_processor: Callable[..., ASLProcessor], tmp_path: Path
+    ) -> None:
+        """An unsupported extension raises ValueError during grouping."""
+        bad = tmp_path / "weird.xml"
+        bad.write_text("<x/>")
+        proc = make_processor(files=[str(bad)])
+        with pytest.raises(ValueError, match="Unsupported file format"):
+            proc._group_files("nifti")
+
+
+# ---------- _group_files: DICOM mode (substring matching for m0) ----------
+
+
+class TestGroupFilesDicomMode:
+    def test_dicom_mode_uses_substring_for_m0(
+        self, make_processor: Callable[..., ASLProcessor], tmp_path: Path
+    ) -> None:
+        """In DICOM mode, any filename containing 'm0' counts as M0."""
+        asl_json = tmp_path / "scan_dump.json"
+        asl_json.write_text(json.dumps({"M0Type": "Separate"}))
+        m0_json = tmp_path / "scan_m0_dump.json"
+        m0_json.write_text(json.dumps({"EchoTime": 0.012}))
+
+        proc = make_processor(files=[str(asl_json), str(m0_json)])
+        groups = proc._group_files("dicom")
+        assert len(groups) == 1
+        assert groups[0]["asl_json"][0] == "scan_dump.json"
+        assert groups[0]["m0_json"][0] == "scan_m0_dump.json"
+
+
+# ---------- _validate_tsv_data: missing TSV behavior ----------
+
+
+class TestMissingTSV:
+    def test_missing_tsv_in_nifti_mode_errors(
+        self,
+        make_processor: Callable[..., ASLProcessor],
+        make_context: Callable[..., ProcessingContext],
+    ) -> None:
+        """Missing aslcontext.tsv in NIfTI mode produces a missing-file error."""
+        proc = make_processor()
+        ctx = make_context()
+        group = {
+            "asl_json": ("asl.json", {"M0Type": "Absent"}),
+            "m0_json": None,
+            "tsv": None,
+        }
+        proc._validate_tsv_data(group, ctx, "asl.json", group["asl_json"][1], "nifti")
+        assert any("aslcontext.tsv" in e and "missing" in e for e in ctx.errors)
+
+    def test_missing_tsv_in_dicom_mode_falls_through_to_dicom_repetitions(
+        self,
+        make_processor: Callable[..., ASLProcessor],
+        make_context: Callable[..., ProcessingContext],
+    ) -> None:
+        """Missing TSV in DICOM mode delegates to _analyze_dicom_repetitions."""
+        proc = make_processor()
+        ctx = make_context()
+        asl_data = {"lRepetitions": 10}
+        group = {"asl_json": ("asl.json", asl_data), "m0_json": None, "tsv": None}
+        proc._validate_tsv_data(group, ctx, "asl.json", asl_data, "dicom")
+        # _analyze_dicom_repetitions sets total_acquired_pairs from lRepetitions/2
+        assert ctx.total_acquired_pairs == 5
+        # No TSV-missing error in DICOM mode
+        assert not any("aslcontext.tsv" in e for e in ctx.errors)
+
+
+# ---------- FileReader: TSV header enforcement ----------
+
+
+class TestFileReaderTSVHeader:
+    def test_valid_header_returns_data(self, tmp_path: Path) -> None:
+        """A 'volume_type' header with rows returns the rows as a list."""
+        from pyaslreport.io.readers.file_reader import FileReader
+
+        f = tmp_path / "valid.tsv"
+        f.write_text("volume_type\ncontrol\nlabel\n")
+        result = FileReader.read(str(f))
+        assert result == ["control", "label"]
+
+    def test_invalid_header_raises(self, tmp_path: Path) -> None:
+        """A header that isn't exactly 'volume_type' raises RuntimeError.
+
+        NOTE: FileReader.read re-wraps the inner error as
+        'Error reading file: Invalid TSV header, ...'. The substring match below
+        still matches; do NOT anchor this regex with '^'.
+        """
+        from pyaslreport.io.readers.file_reader import FileReader
+
+        f = tmp_path / "bad.tsv"
+        f.write_text("volume_types\ncontrol\nlabel\n")  # plural, wrong
+        with pytest.raises(RuntimeError, match="Invalid TSV header"):
+            FileReader.read(str(f))
+
+    def test_empty_file_returns_none(self, tmp_path: Path) -> None:
+        """A truly empty TSV returns None rather than raising."""
+        from pyaslreport.io.readers.file_reader import FileReader
+
+        f = tmp_path / "empty.tsv"
+        f.write_text("")
+        assert FileReader.read(str(f)) is None